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- PDB-9snj: Mus musculus acetylcholinesterase in complex with N-(2-methoxyben... -

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Basic information

Entry
Database: PDB / ID: 9snj
TitleMus musculus acetylcholinesterase in complex with N-(2-methoxybenzyl)-2-(1-methyl-1H-indol-3-yl)ethan-1-amine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Reversible / inhibitor / insecticide
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / collagen binding ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / collagen binding / side of membrane / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEkstrom, F. / Forsgen, N. / Linusson, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2017-00664 Sweden
CitationJournal: Rsc Med Chem / Year: 2025
Title: Potent and selective indole-based inhibitors targeting disease-transmitting mosquitoes.
Authors: Rajeshwari, R. / Duvauchelle, V. / Lindgren, C. / Stangner, K. / Knutsson, S. / Forsgren, N. / Ekstrom, F. / Kamau, L. / Linusson, A.
History
DepositionSep 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,5909
Polymers119,5292
Non-polymers2,0617
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-14 kcal/mol
Surface area37640 Å2
Unit cell
Length a, b, c (Å)79.493, 112.581, 227.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 59764.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#2: Chemical
ChemComp-A1JO2 / ~{N}-[(2-methoxyphenyl)methyl]-2-(1-methylindol-3-yl)ethanamine


Mass: 294.391 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C19H22N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 26-30 % PEG 750 MME 0.1 M HEPES pH 7.0-7.2 / PH range: 7.0-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979957 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979957 Å / Relative weight: 1
ReflectionResolution: 2.3→29.27 Å / Num. obs: 190385 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.39 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.085 / Net I/σ(I): 8.4
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 14316 / CC1/2: 0.894 / Rsym value: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.27 Å / SU ML: 0.1879 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2033 1798 1.97 %
Rwork0.1795 89442 -
obs0.18 91240 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 135 358 8828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318774
X-RAY DIFFRACTIONf_angle_d0.566311993
X-RAY DIFFRACTIONf_chiral_restr0.04331267
X-RAY DIFFRACTIONf_plane_restr0.00531568
X-RAY DIFFRACTIONf_dihedral_angle_d15.74893133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.28251420.2386738X-RAY DIFFRACTION99.29
2.36-2.430.2531380.22596765X-RAY DIFFRACTION99.52
2.43-2.510.2481020.21296861X-RAY DIFFRACTION99.51
2.51-2.60.22831550.20046769X-RAY DIFFRACTION99.5
2.6-2.70.27081510.19896784X-RAY DIFFRACTION99.43
2.7-2.830.2571330.20276824X-RAY DIFFRACTION99.47
2.83-2.980.24541350.20486814X-RAY DIFFRACTION99.71
2.98-3.160.19391500.19726849X-RAY DIFFRACTION99.74
3.16-3.410.23661320.20526903X-RAY DIFFRACTION99.94
3.41-3.750.19881410.18046921X-RAY DIFFRACTION99.87
3.75-4.290.18011380.15466933X-RAY DIFFRACTION99.94
4.29-5.40.15961360.14467016X-RAY DIFFRACTION100
5.4-29.270.18841450.17647265X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9872620214650.320943208091-0.2724095029921.23780460775-0.5200470725713.13670559881-0.141914764803-0.3267773294710.04121500394160.2557577293220.0308670264329-0.01325995353240.05787496933750.1357194004720.1197316591810.5446150877840.0071447178572-0.03480566945520.5422235511530.01540501908380.43093098639131.425794046615.493595123233.8411214752
20.94510721320.346437714806-0.0769343670820.681786314382-0.470332060261.79290518626-0.0680264984404-0.00119237725768-0.0724299051037-0.0217151754854-0.0137290099596-0.08040925238080.2692944099150.1389507325690.09102626057660.579903559430.03452709172340.01856255417160.4806744461320.03856684203780.43851498314835.7104472688.5695797281117.8999809136
31.017509207390.0671517307026-0.1051780131841.06183612643-0.8446509688023.27520315772-0.07164941065860.09436772146460.0421437138548-0.1151633516020.07562300868450.07921305498090.0497549032987-0.325958727187-0.003027175462360.464050813249-0.0399509609968-0.02856664051930.5067951651470.009676587036370.39876088909818.404985348316.97839183186.89782594722
43.99806585557-1.521923684413.685894085652.20229558176-1.728362884243.55908224442-0.0762769847453-0.239827858816-0.6440582762260.2064718425460.3400870157690.3563772832710.501346829829-0.881103305185-0.2754488917790.737138124655-0.281542319860.02840639074660.7393971797180.05992848771370.5568329319346.904291969231.0795123366714.7357376318
52.35864277605-0.716562028371-3.935526871811.886989953352.047432223979.15535960851-0.09678700433390.1797039936060.0842712936642-0.3153970838460.1435198353360.04945956465750.441627741701-0.409350899250.05266106985080.629158812642-0.0839162971617-0.09365982014410.6664162465190.02561129567920.41640373160917.40805752646.43024857203-0.643772168451
62.81410368851-0.610988731822-1.423371459951.541310472170.5697861927144.05631143522-0.05576815076370.3828416902670.180073976506-0.305120128775-0.1491065208450.229780453113-0.103155483715-0.4594236258250.1816155067830.5603399206970.0418408089843-0.1155700307260.598994467832-0.1800608392620.408489951159-3.953212305065.99879013939-61.7907867349
70.157290266907-0.159165491859-0.2301639411581.932243265330.7577768457722.478307232960.1147790744250.184638219634-0.0864227535912-0.180340143226-0.2850187547640.2716727438160.339924806049-0.308307694110.1593587895940.616473870019-0.0242397672097-0.05596436090220.692772358624-0.1264018916080.4650450603932.306389715850.10492378526-53.2884843001
81.48914181518-0.3822705306680.3717138361011.822705514970.2819307030541.940469044630.1485336518010.108795813839-0.0703396437848-0.139867524391-0.1726328293410.0912159161275-0.02482614305070.007835347968450.02539091115340.5531622728510.0182242812993-0.006146549135740.561868051743-0.08584849585160.387355636578.782786835378.66934282419-48.2050736342
91.933706462321.582791063611.20477103363.878978633112.388473259133.394945382860.1075339535820.222640685133-0.15952551330.009394348296260.113393908833-0.02765121428450.4943203882370.526510236198-0.2116701124840.7168991590050.206680255106-0.1187259099880.699126545214-0.07568495389870.47475114396325.4022067938-9.98908729265-49.4653448471
101.80746371293-0.862779816752-0.4397765806312.499813336651.004912968992.339826622250.1301200972890.1054106063760.0813073211150.108845729815-0.102420691204-0.1480902014120.1761036328630.227188226234-0.02683458064560.570689969181-0.031672783663-0.03760561950430.617379827728-0.04557606569060.45111644048818.32052761779.62102693563-38.442654945
111.164403725340.1055729381360.5080960535291.258747818040.1916060222062.173619715930.216164612297-0.265344183867-0.1203335528230.324180923632-0.2402386296060.1906230973530.490999341062-0.2697215755360.01361893803120.625396793077-0.1550860310630.06201868394020.559215146688-0.1059347163720.4002107361584.569743566452.0633672483-26.7482003304
121.695861830352.269046066531.682020289818.03591102452-1.345769767085.649759265920.0234156656873-0.4450367781190.6310156296080.0752125319568-0.03985079218020.631927710892-0.445971954921-0.763004281531-0.05954063350340.6431657986410.01645622918090.07746625766730.758613324645-0.1824518149780.587287710704-1.4654465479922.3418798879-28.7573796321
132.646067054140.1685665106042.259443634681.119210266480.8473358092383.56153786806-0.0110425010108-0.405606642181-0.1506602878520.194399932156-0.07932262773410.05086097196960.1416736039940.1257920136730.08715281741620.714557414642-0.1348131900170.04796110569820.633810877412-0.00848188742580.41206358992813.032607060211.3492777225-21.5212102996
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 118 )AA1 - 1181 - 118
22chain 'A' and (resid 119 through 324 )AA119 - 324119 - 317
33chain 'A' and (resid 325 through 486 )AA325 - 486318 - 479
44chain 'A' and (resid 487 through 513 )AA487 - 513480 - 506
55chain 'A' and (resid 514 through 542 )AA514 - 542507 - 535
66chain 'B' and (resid 4 through 45 )BF4 - 451 - 42
77chain 'B' and (resid 46 through 118 )BF46 - 11843 - 115
88chain 'B' and (resid 119 through 240 )BF119 - 240116 - 237
99chain 'B' and (resid 241 through 288 )BF241 - 288238 - 278
1010chain 'B' and (resid 289 through 331 )BF289 - 331279 - 321
1111chain 'B' and (resid 332 through 486 )BF332 - 486322 - 476
1212chain 'B' and (resid 487 through 513 )BF487 - 513477 - 503
1313chain 'B' and (resid 514 through 543 )BF514 - 543504 - 533

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